The Italy captain was caught in no-man's land early on, allowing MatsHummels to poke goalwards only to see Andrea Pirlo scramble the ball off the line.
Polish striker Robert Lewandowski has been linked with a move to the English Premier League and central defender MatsHummels is routinely mentioned as a potential target for Barcelona.
And when Jakub Blaszczykowski stretched their lead four minutes after the break from a pass by defender MatsHummels it looked all over a victory for the men in yellow.
Juergen Klopp's men should have added to their tally but with 13 minutes left MatsHummels fouled Kevin Volland to concede a penalty and also limped off with a turned ankle, leaving him a possible doubt for next week's final.
Former Bayern defender MatsHummels headed the hosts ahead in the 10th minute from Nuri Sahin's free-kick, but Mario Gomez leveled 10 minutes before halftime as the striker made up for an earlier miss from Arjen Robben's cross by netting from close range.